I changed out the shifter housing/cable because I felt some friction, and ever since it seems like I can't get the indexing right. If I set it to work well in the high gears, it doesn't work properly in the low gears, and vice versa. It worked fine with the old one (which I indexed myself couple months ago), and the only thing I touched is the housing and the cable.
The derailleur, freewheel, and chain are only couple months old, so I don't think they would be the issue. Although weirdly enough, my chain checker did say it's stretched to 0.5 level. I tried replacing the derailleur hanger and cleaned the whole drivetrain in the process, but no luck. Anyone had a similar issue before?